With its language of gold commanders and strategic co-ordination groups, the official response to the latest flooding can sound deeply confusing. Those involved, however, insist the system works well, even if the notion of who is in overall charge remains a slightly elusive one.

"It's like a collective," a Surrey police spokeswoman said when asked who ultimately led the response to floods around the Thames. "Each of the agencies has a representative and they sit on a strategic co-ordination group. It is chaired by the police, but each representative is responsible for their area of business."

Whatever the criticisms of locals who feel abandoned by emergency services, this system came from a period of genuine chaos during events such as the fuel protests in 2000 and the foot and mouth outbreak the next year. The subsequent Civil Contingencies Act dictates what happens during emergencies and tries to ensure various authorities co-ordinate.

With the Thames floods, the process began with the Flood Forecasting Centre (FFC), jointly run by the Environment Agency and Met Office, whose alert at the weekend prompted a series of conference calls with government departments.

The next step was a meeting of the government's Cobra emergencies committee, which has discussed little else in recent weeks. John Curtin, head of incident management for the Environment Agency, has attended 17 Cobra meetings in the last month and a half. As with all attendees, Curtin is not allowed to discuss who attends or what is discussed but called them as "a team, collective effort", rather than a top-down dissemination of orders.

A spokeswoman for the Cabinet Office, which administers Cobra, described it similarly: "It is a mechanism, if you like. Round the Cobra table are all the key people that need to be there to be able to make things happen – ministers, senior officials, people from outside government. Things are discussed there and they can immediately take it away."

The scope of Cobra can be far reaching, ranging from David Cameron, who chaired yesterday's meeting on the floods, to emergency services commanders on the ground via telephone.

It is the latter, the spokeswoman said, who ultimately decide what happens: "The people who are in charge are the ones on the ground. They know what's happening in their area. They know what resources are required. Cobra has a much higher-level role in ensuring that if there are resources that they need and it needs a government department or another organisation to bring that to bear."

Efforts on the ground are organised using a method initially devised by police, with so-called gold, silver and bronze commanders. The gold level has seen top staff from the Environment Agency, police, fire service, local councils, and the military, meet regularly – often several times daily – at strategic co-ordination groups, usually chaired by the police command.

Those involved insist the system has worked well in the Thames floods. But people in Wraysbury, the partially submerged Berkshire village, talked bitterly of volunteer teams rescuing neighbours from chest-deep water, and a severe shortage of sandbags. There is certainly some force to the claims, not least after the noisy complaints saw more than 100 troops descend the next day with supplies.

Paul Southern, assistant chief fire officer at Berkshire fire service, said one reason his crews didn't come to Wraysbury were they were not always called: "We would say that wading in chest-deep water is not the best thing to do as a volunteer. That's the kind of thing that we're here for. If someone had dialled 999 and asked us to go to that we would have been there. But we can't go unless people ask."

Curtin argues the importance of the wider picture: "They key is that you are inherently dealing with the chaos of a natural disaster. What people rarely see is how much worse it would have been without that response.

"This country has just gone through the two biggest surges in a generation and the wettest winter in 250 years."